Summaries of Affymetrix GeneChip probe level data.

By Rafael A. Irizarry, Benjamin M. Bolstad, François Collin, Leslie M. Cope, Bridget G. Hobbs, Terence P. Speed. Nucleic Acids Research, 2003

5,289 citations recorded by the source corpus.

Subfields: Molecular Biology

View Paper: https://www.semanticscholar.org/paper/b8608bff54e1cc933eead9e40c725d7933a567ff

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Citations in the corpus

Multi-omics integration accurately predicts cellular state in unexplored conditions for Escherichia coli (2016, neutral): “The integration method also outperforms the other two individual methods (PCC: 0.41±0.23 for TRN; 0.47±0.23 for KEGG) and is close to that of the CPN method (PCC: 0.52±0.24), although the latter has a 15.4% less coverage.”
PAGE: Parametric Analysis of Gene Set Enrichment (2005, neutral): “For a given microarray data set, use of different methods of data preprocessing, array normalization, and statistical inference can lead to different end results [3,4,29].”
Genome-wide high-resolution mapping and functional analysis of DNA methylation in arabidopsis. (2006, methodology): “First, PM intensities were corrected for background using a convolution model-based method (RMA, available in the Bioconductor package of R) (Irizarry et al., 2003).”
MOLI: multi-omics late integration with deep neural networks for drug response prediction (2019, methodology): “Raw intensities are obtained from ArrayExpress (E-MTAB-3610) for GDSC dataset were RMA-normalized (Irizarry et al. , 2003), log-transformed and aggregated to the level of genes.”
Oct4-induced pluripotency in adult neural stem cells. (2009, methodology): “Normalization was calculated with RMA algorithm (Irizarry et al., 2003) implemented in R-Bioconductor.”
Maternal Immune Activation Alters Fetal Brain Development through Interleukin-6 (2007, methodology): “Determination of expression levels and scaling were performed using Robust Multi-array Average (Irizarry et al., 2003a,b).”
FoxA1 translates epigenetic signatures into enhancer-driven lineage-specific transcription. (2008, neutral): “Gene expression data were normalized and summarized using RMA (Irizarry et al., 2003) and updated RefSeq probeset definitions (Dai et al., 2005).”
Model-based variance-stabilizing transformation for Illumina microarray data (2008, methodology): “Currently, there is no spike-in data set (15) available for the Illumina platform.”
Complex trait analysis of gene expression uncovers polygenic and pleiotropic networks that modulate nervous system function (2005, methodology): “Our mapping results here used the relatively conservative RM”
GSVA: gene set variation analysis for microarray and RNA-Seq data (2013, methodology): “Each remaining Affymetrix chip was background adjusted, normalized and log2 transformed using the Robust Multi-array Average (RMA) algorithm [62].”
The Arabidopsis NFYA5 Transcription Factor Is Regulated Transcriptionally and Posttranscriptionally to Promote Drought Resistance[W] (2008, methodology): “We normalized expression profiles with the RMA method (Irizarry et al., 2003).”